DelPhi Force calculates the forces of atoms/residues on the "target" molecule under the electrostatic field generated by the "reference" molecule. For more detailed instructions, please check our paper and tutorial.
Standard PQR format contains the following information for each atom: index, name, residue name, 3D coordinates, charge, radius. You can generate a PQR file using a PDB file and our DelPhipKa webserver. This will allow you to create a PQR at desired pH.